Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice

Theoretical and Applied Genetics

Volumn 108, Issue 3, 2004, Pages 392-400

  Li, Can ^a   Zhang, Yu ^a   Ying, Kai ^a   Liang, Xiaolei ^a   Han, Bin ^a  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; DNA; GENES; GRAIN (AGRICULTURAL PRODUCT);

BASE PAIRS; CENTROMERE; SEQUENCE VARIATIONS;

GENETIC ENGINEERING;

ARTICLE; CHROMOSOME MAP; COMPARATIVE STUDY; DNA BASE COMPOSITION; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENETIC VARIABILITY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RICE; SPECIES DIFFERENCE; VARIABLE NUMBER OF TANDEM REPEAT;

BASE COMPOSITION; BASE SEQUENCE; CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; MINISATELLITE REPEATS; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS);

EMBRYOPHYTA; JAPONICA; ORYZA SATIVA;

EID: 1542380927     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-003-1457-z     Document Type: Article

References (29)

1. Akagi H, Yokozeki Y, Inagaki A, Fujimura T (1996) Microsatellite DNA markers for rice chromosomes. Theor Appl Genet 94:61-67
2. Barry G (2001) The use of the Monsanto draft rice genome sequence in research. Plant Physiol 125:1164-1165
3. Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537-545
4. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553-567
5. Chen X, Cho YG, McCouch SR (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Genet Genomics 268:331-343
6. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, Park WD, Ayres N, Cartinhour S, McCouch SR (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713-722
7. Feng Q, Zhang YJ, Hao P, Wang SY, Fu G, Huang YC, Li Y, Zhu JJ, Liu YL, Hu X, Jia P, Zhang Y, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Lu Y, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Zhang Y, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (2002) Sequence and analysis of rice chromosome-4. Nature 420:316-320
8. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, T Migue, Paszkowski U, Zhang S, Colbert M, Sun W, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296:92-100
9. Han B, Xue YB (2003) Genome-wide intraspecific DNA-sequence variations in rice. Curr Opin Plant Biol 6:134-138
10. Jakupciak JP, Wells RD (1999) Genetic instabilities in (CTG·CAG) repeats occur by recombination. J Biol Chem 274:23468-23479
11. Jurka J, Pethiyagoda C (1995) Simple repetitive DNA sequences from primates: compilation and analysis. J Mol Evol 40:120-126
12. Kashi Y, King D, Soller M (1997) Simple sequence repeats as a source of quantitative genetic variation. Trends Genet 13:74-78
13. McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199-207
14. Olufowote JO, Xu Y, Chen X, Park WD, Beachell HM, Dilday RH, Goto M, McCouch SR (1997) Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 38:1170-1176
15. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597-607
16. Richards RI, Sutherland GR (1992) Dynamic mutations: a new class of mutations causing human disease. Cell 70:709-712
17. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang J, Gojobori T (2002) The genome sequence and structure of rice chromosome-1. Nature 420:312-316
18. Sia EA, Jinks-Robertson S, Petes TD (1997) Genetic control of microsatellite instability. Mutat Res 383:61-70
19. Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697-712
20. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch SR (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency length, variation transposon associations and genetic marker potential. Genome Res 11:1441-1452
21. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967-981
22. Tautz D, Trick M, Dover G (1986) Cryptic simplicity in DNA is a major source of genetic variation. Nature 322:652-656
23. Wells RD (1996) Molecular basis of genetic instability of triplet repeats. J Biol Chem 271:2875-2878
24. Wells RD, Bacolla A, Bowater RP (1998) Instabilities of triplet repeats: factors and mechanisms. Results Problem Cell Diff 21:133-165
25. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T (2002) A comprehensive rice transcript map containing 6,591 expressed sequence tag sites. Plant Cell 14:525-535
26. Wu KS, Tanksley SD (1993) Abundance polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225-235
27. Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RM (1994) Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245:187-194
28. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92
29. Zhao Q, Zhang Y, Cheng Z, Chen M, Wang S, Feng Q, Huang Y, Li Y, Tang Y, Zhou B, Chen Z, Yu S, Zhu J, Hu X, Mu J, Ying K, Hao P, Zhang L, Lu Y, Zhang LS, Liu Y, Yu Z, Fan D, Weng Q, Chen L, Lu T, Liu X, Jia P, Sun T, Wu Y, Zhang Y, Lu Y, Li C, Wang R, Lei H, Li T, Hu H, Wu M, Zhang R, Guan J, Zhu J, Fu G, Gu M, Hong G, Xue Y, Wing R, Jiang J, Han B (2002) A fine physical map of the rice chromosome-4. Genome Res 12:817-823